Fragment Collection

One of the powerful features of DNA and RNA chromatography is that material can easily be purified by collecting directly from the detector effluent Purification can be used in biological samples, where there may be several types of nucleic acids present and a particular type is desired for study. An example of this is shown later in this chapter where several types of RNA are detected in a cell extract and can be purified. 

---

The comparisons with experimental distributions would be incomplete without examining some exploding munitions data. Data of this type have been published by Mock and Holt (1983) in which explosive-filled cylinders of armco iron and several heat-treated steels were detonated, and the fragments collected and analyzed. A cumulative number distribution from one of the heat-treated steel experiments is shown in Fig. 8.33. The trend of the data in this example is typical of the six experiments performed by them. 

Of course protecting the reactive functionality of a compound alters its binding characteristic. Therefore, selecting the reactive monomer types to be included in a fragment collection and selecting its protecting group must be carefully considered and chosen wisely. 

In the following sections, we will describe in detail efforts to build fragment collections and the processes involved in their creation. Two such efforts were performed at a major pharmaceutical company (Pfizer) while a third took place at a biotech company (Vernalis). 

Selection of the reagents was based on the Pfizer internal compound collection which allowed speedy acquisition of any selected compound. A set of primary amines, secondary amines, and carboxylic acids which were not commercially available were chosen for consideration. These acids and amines were designed by medicinal chemists via a Pfizer internal screening file enrichment effort to be novel and diverse, and more importantly, were not part of any existing Pfizer fragment collection. The MW... 

Approximately 1,200 amines and 300 carboxylic acids were selected for inclusion in the fragment libraries, from which approximately 20 fragment libraries were synthesized. These libraries yielded 2,000 products with sufficient purity (>95%) and quantity (1.2 mL of 30 xM solution), and the product structures were confirmed via ID NMR. This fragment collection became known as the NMR Combicores to denote their purpose and their combichem origin. It was distributed across several major Pfizer research sites and used in multiple fragment screens. 

Due to the evolutionary nature of the Vernalis fragment collections and the fact that various screens were performed over a period of several years, it is difficult and perhaps unreasonable to directly compare the hit rates across multiple screens. However, it is still helpful to notice that reasonable hit rates (compared to HTS) are obtained across a diverse group of targets (Table 11.1). 

The importance of physicochemical properties and structural diversity to the assembly of a successful fragment collection has been described in earlier sections. In this section, we will focus on an interesting analysis done on the distribution of the physicochemical properties and 3D pharmacophore triplet in three groups of molecules hits, nonhits, and the whole library. Hits are defined as fragments which have been identified as... 

Over the past several years, descriptions of fragment collections have been published in journals as well as book chapters. In two recent reviews, a chapter from Evotec (33) compared several collections based their origins, while a journal article from Leiden University (26) summarized fragment collections based on the intended screening methods. We would like to present an overview by blending information from both reviews together to provide a more complete and updated picture (see Table 11.2 for details). 

Fig. 15.1-6 Selected fragment screening experiment applied to proteases and kinases. In their landmark study, Fesik et al. equilibrated hydrophobic molecules with stromelysin and detected binding by shift of NMR signals, retrieving structural information from the initial study [66]. Other studies screened fragment collections using...

Numbers in parentheses indicate fragments collected from hot deserts and Queen Maud Land Antarctica, uncorrected for pairing except for Lunar and Martian samples. 

Figure 18. Typical XRF spectra of 10 pm regions of bone from turtle shell fragments collected from two contaminated sites and the control site (Reprinted with permission of EDP Sciences from Hunter et al. 1997, Fig. 1.)...

---